In 20xx, a mummy of a giant kaiju is salvaged in the north sea of Hokkaido. Shinichi Ozaki, a mutant soldier of the M-Force, investigates the mummy with Miyuki Otonashi who is a biologist sent from the UN.
At that time, Kaijus appear in cities all over the world simultaneously! New York, Paris , Shanghai, Sydney -- Kaijus appear one after another!
The earth defense force invests the full war potential, but they can only fight defensively because of too many kaijus.
Among the world-wide confusion, an airplane of Naotarou Daigo, who is a Secretary General of the UN disappears.
The earth defense force fights desperately, but cannot defeat the kaijus. Ozaki, who arrives on the sight of a kaiju arrival, strives to fight against the kaiju with another mutant soldier Kazama by using their super physical powers.
Among the intensive battles all over the world, UFOs suddenly appear in the sky, and eliminate the kaijus. UFOs are concentrated above the base camp of the earth defense force in Japan, and Daigo, the missing Secretary General of the UN appear from the UFOs. He suggests a friendly term with the aliens who introduce themselves as "X-seijin(X-Aliens)". The heads of the world decide to form an alliance with the X-Aliens.
However, Ozaki and Miyuki have a doubt about X-Aliens and researched their nature with Miyuki's elder sister Anna. While researching, they ask assitance from the captain of "Kaitei Gunkan Gouten-gou (Atragon)". Now the final wars of Ozaki and his companions on the Atragon start!
Godzilla keeps sleeping in the ice of south pole at that time ......
